diff metaphlan2.xml @ 25:e8e0f835b4b6 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 11b919f18ba85a40ff0ff4df82aac9be6da188c5-dirty

--- a/metaphlan2.xml	Wed Dec 09 11:48:33 2015 -0500
+++ b/metaphlan2.xml	Thu Mar 31 03:25:48 2016 -0400
@@ -1,10 +1,10 @@
-<tool id="metaphlan2" name="MetaPhlAn2" version="0.1.0">
+<tool id="metaphlan2" name="MetaPhlAn2" version="2.2.0">
 
     <description>to profile the composition of microbial communities</description>
 
     <requirements>
-        <requirement type="package" version="2.2.4">bowtie2</requirement>
-        <requirement type="package" version="2.0">metaphlan2</requirement>
+        <requirement type="package" version="2.2.5">bowtie2</requirement>
+        <requirement type="package" version="2.2.0">metaphlan2</requirement>
     </requirements>
 
     <stdio>
@@ -26,13 +26,19 @@
     </version_command>
 
     <command>
-<![CDATA[
+<![CDATA[        
+        (which bowtie2 || exit 200)
+
+        &&
+
         python \${METAPHLAN2_DIR}/metaphlan2.py
             $input_file
             -o $output_file
 
             --input_type ${input_file.datatype.file_ext}
             --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl 
+
+            --bowtie2_exe `which bowtie2`
             --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
 
             --no_map
@@ -117,7 +123,7 @@
     </inputs>
 
     <outputs>
-        <data format="txt" name="output_file" 
+        <data format="tabular" name="output_file" 
             metadata="input_sequence_file" 
             label="Profile of communities on ${on_string} (MetaPhlAn)" />
 
@@ -145,8 +151,8 @@
             <param name="ignore_bacteria" value="" />
             <param name="ignore_archaea" value="" />
             <param name="stat_q" value="0.1" />
-            <param name="sam_output" value='False' />
-            <param name="biom_output" value='True' />
+            <param name="sam_output" value='false' />
+            <param name="biom_output" value='true' />
             <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/>
             <output name="biom_output_file" file="metaphlan2_biom.biom"/>
         </test>